On these newer Macs, EyeTV can also be controlled by the Apple Remote. Specifically, you can use the Apple Remote to call up EyeTV’s new Full Screen Menu...The Apple Remote only works with the Mac’s built in IR sensor and can not be used with IR Sensors on EyeTV devices.

So although you can use the Apple Remote to control EyeTV, it will only work if you have a built-in IR receiver

I just went to Twisted Melon's site. They are touting the Manta TR1 which enables you to use the apple remote with older Macs. This is a good backup plan, but it would be nice if I didnt have to buy new hardware, after all, I have everything I should need, it's just the software configuration that is stopping me.